Pokémon: Extinction
by The Troubled Writer
Summary: A bizarre and frightening race of creatures have invaded the peaceful Pokémon Island. Facing certain death and extinction, the wild Pokémon must band together in order to stop a threat that endangers their entire existence. Chapter 3 is on its way!
1. Prologue

PROLOGUE: A VERY BRIEF INTRO

Welcome to Pokémon Island! Here, wild Pokémon live in the island zones, free from the constraints of a PokéBall and Trainer battles. For decades, Trainers have been steered clear of this area, as it is a wildlife preserve, a place dedicated to the growth of natural Pokemon. It was set up by the Wild Pokemon Preservation Community to stabilize the Pokémon population, saving their lands instead of converting them into new cities or highways. On these islands, it is the only place Pokémon are able to live truly free. They are not spread into grassy areas in towns for Trainers to catch them, and because of that, they are much stronger than the average city Pokémon, growing up on their instincts rather than the tenderness and bonds they share with their Trainers.

Located in the Serenity Ocean, the chain of islands consist of six major islands and several islets that are uninhabited or simply visited by other Pokémon on occasion. For the most part, it is the six major islands that can be seen from space. Tourism is a no-no for the island as Pokémon appreciate their privacy and the WPPC confirms that by only allowing pictures and videos to be taken from afar. And, because of no human contact, there aren't any endangered species of Pokémon struggling to survive.

The climate of these islands are typical for the tropics: hot days and cool nights, though there are other areas that are so extreme in temperature due to the other types of Pokémon that exist here as well, such as Ice and Fire. So, depending on the island, the temperatures vary to a great degree. The famous Legendary Pokémon (as called by Trainers) have never appeared on these islands. On another note, Shiny Pokémon are also 8% higher than in the human cities, where they are bred like machines for their color alteration.

Activists for years have worried about the increasing number of Trainers coming to the various regions and capturing and trading Pokémon to one another. They feared Pokémon would change into mere house pets and not the wild creatures they should be, free to explore and loose of any human contact. They were also worried about the millions of dollars put into Pokémon research and the development of new ways to modify Pokémon, such as the recent Mega Evolution. As a result, the WPPC was forged with thousands of members supporting the right for Pokémon to have their own land and not trapped in the concrete world built by human beings. This may have caused anger in Trainers around the globe, but they were ensured that the WPPC were not attempting to take Pokémon away from Trainers but merely to give them a place where Pokémon could roam as they pleased and not be acquired and trained according to their master's wills. Still, the anger remains.

But those Trainers would be the least of the Pokémon's troubles, after this moment that would change the peaceful islands for an eternity...

All rights reserved, you know how it goes! All Pokemon belong to Nintendo; original ideas belong to me, The Troubled Writer.


	2. Chapter 1

CHAPTER 1

That memory seemed a lifetime ago... Flabébé remembered her clearly as she watched the stars glitter across the night sky, magical orbs of light far from her small arms. She held the pistil of her flower close to her fragile body, wondering what has become of the Trainer that had forsaken her. The only memory she had of her was being caught by her for the first time. They met at a riverside road in the middle of the night. She threw a Poke Ball at it, captured her, and they began to travel together. Flabébé remembered that she got lighthearted, believing they would be the best of friends on their journey together. But as the time went on – days turning into weeks, turning into months – she began to realize that something was amiss. Nevertheless, she still had high hopes that, one day perhaps, she would release her from Cassius's PC so they could play together. The Trainer, alas, released her from the box without saying goodbye to her. Flabébé was not even given the glimpse of her Trainer's face before she was cast off, like a leaf in the wind... She guessed she was not good enough to be loved.

Left behind with nowhere to go, Flabébé often cried herself to sleep, frightened and wanting a home. But no one wanted her, the poor red-petaled Flabébé. She had seen other Trainers with them, haughty and proud of themselves, given treats and played with, loved and cared by them. Her small eyes were so often filled with tears that she believed they would become like this forever. But she had a friend she never knew of, a Pidgeot that came to her rescue one stormy night; Pidgeot found her under a tree, hiding from the pursuing rain. The Pidgeot could see the great fear and scare in her small eyes.

"Don't be alarmed, I am here to help you," Pidgeot said. She offered one of her great wings for help. "Come on."

Flabébé wanted badly to flee the rain so she hopped aboard her back and they began to fly far from the dripping tree. The Pidgeot's hair was what struck Flabébé, the stretching yellow with pink stripes; it looked strong, as well as pretty.

"Where are you taking me?" Flabébé asked.

"Somewhere safe from them," was all Pidgeot replied, speaking scornfully about them humans.

"Did something happen to you too?" Flabébé questioned again.

And, for a time, Pidgeot was quiet. At last, she spoke when the rain began to lose speed. "I'll tell you about it when we get there."

"Okay."

She was unaware of where she was being taken, but she was silent all the while, not wanting to be argumentative about it. Her home was already gone from her, she might as well accept the new place the Pidgeot was bringing to her...though that did not stop her from looking back one last time towards the civilization behind her. Somewhere in those towers was where her old Trainer was, probably having fun with another Flabébé. That thought nearly made her cry again, and how would Pidgeot know the difference? The tears would blend in with the light patter of the cloud's weeping anyway.

And then they were there, where the Pidgeot was flying her to. She saw a huge island resting in the water; was this to be her new home? The rain had disappeared by this time, and no sooner did Flabébé realize that, the Pidgeot swooped fiercely down, jetting to the islands. Flabébé was nearly thrown off, and her flower's petals nearly fluttered away. But all was well when they touched the ground and Flabébé was able to jump off the Pidgeot's back safely, leaving one world and entering another one. Flabébé's eyes floated in wonder at the trees, the water, the mountains, everything that she could see; and the surprise to her was that there was more!

"What is this place?" Flabébé asked, trapped in the wonderment of this foreign place.

"Does it matter? All that you should care about is that it is your home, not a Trainer's." There goes that insulting tone again that bit into the peaceful atmosphere.

Flabébé looked back at her. "You told me you would tell me what happened to you when we got here, remember?"

The Pidgeot nodded, furious still. "That I did. Come, I will tell you, as promised."

And the Pidgeot's story began. She told Flabébé that her trainer was abusive to her after being traded from her original Trainer, a trade she wished never happened. After one particularly terrible altercation with the Trainer, the Pidgeot flew out of a battered window, never returning to him. Months afterward, she searched for her previous Trainer but could not find him. Assuming he was gone, the Pidgeot flew aimlessly for days before discovering the Pokemon islands for herself, and a relief washed over her, a feeling of finding home again. And she discovered her happiness there, even without the presence of a Trainer.

It was here that would become Flabébé's new home. _So long Trainer..._

"Away we go now," the Pidgeot said to her in a motherly way, inviting Flabébé to her wings. She would be her protector, her surrogate mother, her Trainer. Before they took off, Pidgeot looked at her, saying, "Welcome home."

Home it was indeed, living with Pidgeot and her family of Pidgeys; Flabébé had never been so cheerful before, enjoying her time with the other wild Pokemon, ones she had never seen before, of all colors and shapes. Several of their stories were also sad, like the Pidgeot's, but some were not as they were just born on the island and did not emigrate to the islands due to abandonment or running away from a bad Trainer. Because of all these good times she was having, there were days when she completely forgot about the Trainer that released her. Days such as those came by, without a doubt, but she was able to deal with them much better the more time went on, and those emotional feelings about her began to rescind.

But, of course, what would life be without death?

The Pidgeot that took care of her eventually died of old age. She was buried within a soft little mound where the sun could be seen clearly rising and falling each day. It was here she was buried because this was where she first set foot on the island, where her happiness was found again.

As was the case with Flabébé.

But now, she did not think of that sadness, only of the stars glittering above in the great night sky, wondering if she was there too, watching over them. Would she be watching Flabébé? She hoped so.

However, something came by that suddenly distracted her from those thoughts. A green meteor suddenly shot through the night sky, dashing by the stars, streaking it brightly. Flabébé opened her mouth in awe of the thing in passing. She froze as she watched the meteor dash by.

"What _is _that?" she asked, astounded.

She followed it with her eyes, as it descended closer and closer to the earth. The bright green falling star illuminated the entire sky for a brief moment. And then, within seconds, a great explosion came, so loud Flabébé had to cover her head from it; a terrible vibration rattled the ground in its wake. She must have been standing there for several minutes before the violent rumbling came to an end. Then she opened her eyes...and saw the smoke from the impact billow up into the night sky, a tower of black fog.

Flabébé was panicky, trying her best to think of what to do about this. She was amazed and also terrified about this, believing something bad would happen now with the eerie presence of this strange rock somewhere beyond where she stood. Nevertheless, she could not stand still and do nothing about this. Surely the others knew...perhaps _already _knew. Holding tightly to her flower, she hopped away in an excited haste...

Gathered together, Panpour, Pansage, and Pansear were eating berries near a collected fire, under the cloak of trees and the sound of a Hoothoot hooting in the background. Pansage offered Hoothoot some berries but he refused. He was in the middle of hooting...and it was apparent they were not aware of the meteor that just blazed its green tail across the sky and smashed into the earth mercilessly. While Pansear was roasting his fifth berry, Flabébé came exhausted from her trip, flushed, and huffing her breath.

"Hey! Hey!" she called out to them, hopping all the way.

The three turned to her. Panpour – and his eternal smile – waved her over. "Hey! Come on, we have plenty of berries here!" He spread his hand at the mound of berries warming up near the fire.

"Yeah, relax! Have a berry or two," came Pansage. They were all in high spirits this night...but Flabébé was not sure for how long.

"No time," she sighed out. "You have to see this! It came from the sky!"

"What did?" asked Pansear.

"Just come on!"

Pansage, Panpour, and Pansear – not concerned with anything snatching their horde of berries – followed Flabébé to...wherever she was going so she could show them the amazing thing she saw. Panpour lifted her into the crook of his arm and carried her because she was moving a tad slow, but now, at their speed, they journeyed to the open meadow where Flabébé was when the meteor passed. And when they got there...

"Woah!" called the three simultaneously. They saw the sight of the black smoke towering higher into the sky.

"It flew by fast!" Flabébé said. "It was green, and very bright!"

But that was not the only surprise this meteor had for the four of them: a vivid green slowly illuminated the spot of impact, spreading the light for a far distance. The four of them did their best to shield their eyes from the distracting light, before all went to the darkness of night once again. What the purpose of that was, they did not know.

"What do we do?" Flabébé asked them.

They thought for a moment. Something like this does not happen on the peaceful islands; the only invasion they really have to go through is when the tourism season starts up, and they have to be bombarded with people using their camera phones and whatnot to get a glimpse of the islands and any Pokemon they could find. That, they could deal with, but...

"We should tell the others..." Pansear said to the group. "I'm getting a bad feeling about the green light that just came out..." An eerie feeling crossed all of them after he said that.

"Same here," Pansage agreed. "We have to rally up as much of the others as we can. They need to know about this."

Flabébé nodded in agreement with their plan, and began to follow them away from the sight of the strange meteor. But before she did so, she returned her eyes to the stars...because she was unsure if she would ever see them again. Following what Pansear said, she also felt something awful from this intrusion.

They both were not far from the truth...


	3. Chapter 2

CHAPTER 2

Finneon – the Beautifly of the Sea – was swimming along peacefully away from the school of other Finneon (and a few Lumineon), as he usually does during the night, to see if he could spot the stars gleaming above. He believed them to be similar to him: storing the sun's light so they may illuminate brighter in the night. He was the same way, unintentionally stealing rays from the sun for himself, so he may better shine when the waters cooled and became darker...but tonight seemed different from the past nights. It seemed the other Pokémon were in their own placidity, as it was very quiet; not even the waves crashed, not unlike Lugia's storm that occurred nearly two years ago, off the coast of Tranquil Sea. Finneon remembered that disaster, extensive in both land and sea, threatening also the flying Pokémon, some of which were sadly caught in that deadly tempest. The reason why he was remembering this now was because he felt a rumble just now that was very similar to Lugia's storm.

Finneon looked up to see, from the ocean surface below, a green streak shooting across the sky. It rippled and waved, heading closer to the earth. He watched in complete fascination, though he did not know what it was he was seeing. The one thing he knew for certain was that he began to follow it quickly. His fins flapped back and forth and he was speeding the best he could, trailing the mysterious green light. But then, _WHACK_! Finneon smashed his face into Lapras.

Surprised, she looked down to see the flailing Finneon splashing the water. "Are you okay?" Lapras asked.

Finneon shook himself and poked his head out of the water's surface. He only had about a few minutes before he had to dip his face back into the water to breathe again. "Did you see the green thing in the sky?"

Lapras looked up, as if seeing for the first time. "Yes. I've been trying to keep track of it, but it's much too fast for me." She smiled gently at him. "If you wish, you can travel with me."

Finneon nodded. "Okay, okay."

Finneon latched on to Lapras's fin and they began to swim closer to shore. By this time, the green streak began to fade, becoming a green haze that painted the night sky. They were not even that close to shore before a great wave from the impact came rushing across the islands. Lapras stopped, closing her eyes, while Finneon held on to her fin as the shock wave finally passed, and they could see in front of them again. A green energy was rising out of the spot where the meteor crash landed.

"Hurry, let's head over there," Finneon said.

Lapras went ahead. There was Ducklett as well, running on the land, near exhaustion. He saw Lapras and waved to her.

"Did you see that over there?" Ducklett shouted. He sounded ecstatic over what he saw. The green streak was beginning to vanish.

"You'll have to tell us what you see," Lapras told him. "We cannot travel onto the land."

Ducklett nodded; his mission was given to him. "Okay!"

Lapras pulled up onto the shore the best she could, Finneon still holding on to her fin. Finneon peaked one more time to the sky and saw the green light radiating from the earth, and also that other Pokémon were traveling to the meteor crash site. Finneon wished he could join them, but all he could do was watch from afar. He sighed, knowing his limits.

"Not to worry," Lapras told him, as if she could read his thoughts. Her smile made him smile, but only briefly.

"What do you think it is?" Finneon asked.

"I don't know," Lapras told him. "Whatever it is..." For some reason, Lapras was not compelled to finish what she was about to say. It was as if her tongue was caught in a snag. Finneon looked up at her, waiting for her to finish. Then, she shook her head, still not answering him.

But she did not need to, for Magikarp came right on time, poking his orange face out of the water.

"Hey there!" he greeted.

He nearly gave Finneon a fright. "Magikarp! You saw the green light too?"

"There's something else I want to show you!" Magikarp urged. He sunk down into the ocean again in the hopes Finneon would follow...and he did. Lapras remained above the water, watching the other Pokémon investigate this bizarre occurrence.

"What is it?" Finneon asked with little patience. He believed he was missing the good stuff.

"You'll see!" Magikarp teased.

Together they swam down further and deeper into the ocean. Finneon knew he was far from the school he often traveled with, wondering if they knew of this light, or if they merely scattered instead of trying to figure out what it was that entered their island. Thousands of Pokémon lived here, in the land and sea and air; were they in any possible danger? What should they do of the strange rock beaming a freakish bright green light? And what was it that Magikarp wanted to show him so badly?

"There, look!"

Finneon followed, and discovered a shard stabbing the ocean sand, its tip pointing upward. It was _green_, just like the meteor. Finneon swam further, cautiously, to it, examining it all around. Even in the dark ocean, it managed to shine brilliantly.

"This is from the strange light..." Finneon said. He had already connected the pieces...no pun intended.

"It fell with a _SPLASH _in here," Magikarp said. "I tried to pull it out, but I could not do it."

Finneon and Magikarp stared at it together silently. They knew the shard was somehow connected to whatever had fallen its way here. No matter how the Pokémon looked at it, something alien had made its way here. And now that it was here, it could not be avoided or shaken off as some sort of natural happening; there was nothing so ordinary about it, even if they wished it to be.

And that was when the green light flashed spontaneously, blinding the night sky.


	4. Chapter 3

CHAPTER 3

Flying on the updraft from the sea, Wingull glided across the night sky freely. In his beak, he carried a green stone he found floating in a puddle not too far from where the meteor crashed. He was not sure what the stone was, or its purpose, but it was shiny and he took it anyway.

"I wonder what it does..." Wingull asked himself. He was certain nothing would come of this stone...yet he felt something strange from it. Perhaps he should have left it alone... Too late for that now.

Wingull floated down onto his nest, perched upon the sea cliff overlooking a beautiful view of the stars. He was not looking upward, though. He was looking groundward, at the green stone he just spat out. He did not know what to expect from this strangely growing rock, but he liked to look at it. It was very shiny...

"Wingull!" suddenly came two voices simultaneously.

He turned to see Plusle and Minun advancing towards him together. Taking a few scraps from the nest, he placed them on top of the green stone so he could hide it from them. He didn't want them to take it from him.

"Whacha doing?" Plusle asked. She was the red one.

"Did you see the big green thing that came crashing down?" came Minun. He was the blue one.

"What do you think it was?" Wingull asked. He pushed the rock away with his foot.

"Dunno. We're gonna see! Coming?"

Wingull thought quickly. If he came along, it would remove any suspicion they might gain of him but it would leave the green stone unprotected from any thieves. If he decided to stay, they might ask him why and that might lead into them finding the stone he just found... Between these two choices, Wingull decided it best to come along but said he would catch up with them in a bit. He watched them walk away a certain distance before taking his hard-earned stone and digging it deeper into the ground. No one would find it now! He flew away from his nest and followed the cheery Pokémon to wherever they were taking him.

"Shouldn't be too far now!" Minun said aloud. He sounded a bit more excited than he should be. After all, none of the Pokémon on the island know what it is that crash-landed on their island.

Croagunk was on his way there as well. He was traveling alone, walking with a strange gait when he suddenly saw the three Pokémon traveling together. An odd group, he thought. He smiled anyway and walked to them.

"Hey," he said in a croaking voice. "Where ya going?"

"We're going to see the green rock," Plusle told him. "You wanna come along?"

Croagunk looked at them. "That strange thing in the ground? Nah, I'll pass."

"Okay then," Minun said. They were to go on their merry way...

"You should stay away from that rock. I'm getting a bad vibe from that thing."

They all turned to meet Croagunk's eyes, meeting them with his own uncertain eyes.

_Fear would come much later..._

"What do you mean?" Wingull asked.

Before they could get their answer from the toxic mouth Pokémon, a huge explosion rocked the foundation of the island. A large, dome-like green light shone as bright as it could in the far distance, and the four of them began to see the other Pokémon running, fleeing, from the green. They merely stood there, stuck in shock and horror, not moving from the spot while a Rattata had to be held back because he wanted to fight. Sure, he did not know who it was but he still felt a need to defend his home.

"Let me get 'em! Let me get 'em!" he shouted.

Patrat held him back. "We gotta get out of here!"

At last, after more struggling, Rattata agreed and followed Patrat far from the green light. Oddish was also seen running as fast as she could from the green light. She stopped in front of the four, a bead of sweat falling down her head.

"You hafta get out of here!" she squealed.

"What happened?" Minun asked.

"You know that green rock that came down, right? Chimchar tried touching it, and then it went _berserk_! Everyone started running; I don't know if Chimchar got away..."

Plusle came up with an instant plan. "We have to go and help! He may need us!"

"Or maybe he escaped with the rest of them," Croagunk suggested. "No use risking our necks if he got away safely."

"But what if he didn't?" argued Plusle. "He could still be out there, vulnerable and in need!"

More Pokémon were fleeing the scene, although some (like Rattata) tried to destroy the green rock and splinter it into a thousand shards. It did not go as planned. So the stampede commenced while the five were trapped in deciding whether or not they should look for Chimchar. As Croagunk said, there was much risk in taking that option. They still did not know what it was taking its home on their island...or what would come out of it, making the risk even bigger. The other Pokémon agreed, for in this situation, it was about one thing and one thing only: survival.

Chimchar would have to get left behind. They had no choice.

"Come on," Croagunk grabbed Plusle and Minun and ran along with the other Pokémon, against their protests. Deerling was fleeing the scene alongside them. Oddish jumped onto Wingull's offering back and they followed them and the other bird Pokémon to a safer location. Spearow and Pidgey were bickering but also following the horde.

The sound of so many Pokémon running away sounded like thunder if someone were watching from above, all running together in one direction. However, a pair of blue eyes were watching them, high into the clouds. Far from reach and sight. It blinked innocently and then flew off.

Meanwhile, back at ground zero...

The green rock cracked open slowly, as if it were a shell, or perhaps an egg. And from that opening came a bizarre creature with large red eyes, which it used to search its surroundings. It did not say anything, and it did not need too, quite frankly. It knew exactly who it was and what it was meant to do. It felt no remorse for what it will do in the dark future ahead, most likely it did not care. Destruction and mayhem were its only way of life; they were created for no other reason besides those, and it would do anything to complete it, along with the legion that followed this alien.

Its red eyes opened, as did thousands of others.

"Mission activated."

_And to think, this could have all been avoided, had they listened to Absol._

The first three chapters all happen within the same time, in case you were confused in anyway. Thank you.


	5. Intermission

Like a round table, the strongest and most powerful Pokémon in existence sat around in a large circle, their differences pushed aside for this one time only. With the exception of Giratina (who has been re-trapped into the Distortion World), Genesect, Zygarde, Celebi, and Mewtwo, all of the world's Legendary Pokémon were in attendance:

Zapdos, Articuno, and Moltres, the legendary birds;

Raikou, Entei, and Suicune, the legendary beasts;

Lugia and Ho-Oh, the tower duo;

Regice, Registeel, and Regirock, the legendary golems;

Latias and Latios, the eon duo;

Groudon, Kyogre, and Rayquaza, the weather trio;

Jirachi;

Deoxys;

Azelf, Mesprit, and Uxie, the lake guardians;

Dialga and Palkia, only two of the creation trio;

Cresselia and Darkrai, the lunar duo;

Manaphy and Phione, the sea guardians;

Heatran;

Regigigas;

Shaymin;

Arceus, who was at the head of this gathering; Victini;

Cobalion, Terrakion, Virizion, and Keldeo, the swords of truth;

Tornadus, Thundurus, and Landorus, the forces of nature;

Zekrom, Reshiram, and Kyurem, the tao trio;

Meloetta;

And finally, Xerneas and Yveltal, the mortality duo.

It would be just this group, speaking about the coming invasion on the Pokémon Island. Yes, they were aware of what was happening, but what should they do? That is why they are here.

"We are gathered here on this day," spoke the powerful Arceus, standing tall and high, "in the event of this war that will be unleashed upon the Pokémon Island. You all know of that. What will you all say about this?"

"What is the cause?" Cresselia asked. The voice was angelic and soft.

Heatran turned to Deoxys. "An alien virus. Like you."

Deoxys glared at Heatran. "I did nothing to cause this."

"It's an alien race from another dimension," Arceus spoke out, silencing all. "I felt them arrive through the ripples of the universe."

"We should fight," Victini spoke out before the arguing could extend. "They need us."

"Have we not helped them enough?" came Articuno. "We must back off."

Zapdos and Moltres agreed with Articuno's statement.

"There are much Pokemon for us to look after," Azelf said. "Not only on the islands but also where the humans stay. It is too much, even for all of our powers."

"We protect Pokémon from humans. We will not fight in this war," Cobalion said. He spoke nothing but the truth.

"Will they be able to survive against this unknown threat?" Xerneas said. "Maybe our involvement will be beneficial to their cause."

"Let them fight!" Groudon's voice interrupted. "Let them become strong on their own!"

Arceus heard every opinion patiently. There were no concrete sides as all the legendaries had their own opinion about everything involving this conflict. It was safe to say that coming to a conclusion would be difficult.

"These Pokemon need a miracle," Jirachi stated. "I would happy if –"

Regigias rose imperially. "Either way, severe damage to this world will occur. The continents I created will suffer from this world."

"We are all Legendary. If we all interfere simultaneously, the world will grieve much worse than damage to your lands, Gigas. It is possible that all will be reshaped and balance would have to be restored again. Is that a risk we are all willing to take?"

All of the Legends fell soundless. It was their world also that was being tainted by this mysterious force that is now here. And most of them looked toward Arceus with eyes of expectance. They somehow knew what Arceus would say, even if they did not agree with it.

"We must now interfere with this plot," Arceus stated aloud. "This war has come to their lands, but it is not for us to become involved. This apocalypse is not our problem."

Victiny and Shaymin looked surprised, and the same silence permeated through the Universe Hall. Even though some voted to not battle with the Pokemon on the island, these aliens represented a real threat because they were from another universe, another dimension entirely, one even Arceus did not know about until it was too late. It seemed the right decision to lend a helping hand…but Arceus refused.

Rayquaza's glare increased.

"That concludes this meeting," Arceus said at last. "Dismissed."

And just at that moment, Arceus turned and saw Mew dash away...


End file.
